{"id":"https://openalex.org/W4380685989","doi":"https://doi.org/10.3389/fninf.2023.1174049","title":"SNAP: a structure-based neuron morphology reconstruction automatic pruning pipeline","display_name":"SNAP: a structure-based neuron morphology reconstruction automatic pruning pipeline","publication_year":2023,"publication_date":"2023-06-14","ids":{"openalex":"https://openalex.org/W4380685989","doi":"https://doi.org/10.3389/fninf.2023.1174049","pmid":"https://pubmed.ncbi.nlm.nih.gov/37388757"},"language":"en","primary_location":{"id":"doi:10.3389/fninf.2023.1174049","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3389/fninf.2023.1174049","pdf_url":"https://www.frontiersin.org/articles/10.3389/fninf.2023.1174049/pdf","source":{"id":"https://openalex.org/S179816892","display_name":"Frontiers in Neuroinformatics","issn_l":"1662-5196","issn":["1662-5196"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Neuroinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fninf.2023.1174049/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027506122","display_name":"Liya Ding","orcid":"https://orcid.org/0000-0002-1209-875X"},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Liya Ding","raw_affiliation_strings":["Institute for Brain and Intelligence, Southeast University, Nanjing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Brain and Intelligence, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088096437","display_name":"Xuan Zhao","orcid":"https://orcid.org/0000-0002-5778-5422"},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuan Zhao","raw_affiliation_strings":["Institute for Brain and Intelligence, Southeast University, Nanjing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Brain and Intelligence, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025490895","display_name":"Shuxia Guo","orcid":"https://orcid.org/0000-0001-8237-8936"},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuxia Guo","raw_affiliation_strings":["Institute for Brain and Intelligence, Southeast University, Nanjing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Brain and Intelligence, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100376625","display_name":"Yufeng Liu","orcid":"https://orcid.org/0000-0003-0848-5113"},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yufeng Liu","raw_affiliation_strings":["Institute for Brain and Intelligence, Southeast University, Nanjing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Brain and Intelligence, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100343786","display_name":"Lijuan Liu","orcid":"https://orcid.org/0000-0002-9548-6183"},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lijuan Liu","raw_affiliation_strings":["Institute for Brain and Intelligence, Southeast University, Nanjing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Brain and Intelligence, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100384237","display_name":"Yimin Wang","orcid":"https://orcid.org/0000-0003-2515-6602"},"institutions":[{"id":"https://openalex.org/I32820368","display_name":"Guangdong Polytechnic of Science and Technology","ror":"https://ror.org/01wq2p249","country_code":"CN","type":"education","lineage":["https://openalex.org/I32820368"]},{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yimin Wang","raw_affiliation_strings":["Guangdong Institute of Intelligence Science and Technology, Zhuhai, China","Institute for Brain and Intelligence, Southeast University, Nanjing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangdong Institute of Intelligence Science and Technology, Zhuhai, China","institution_ids":["https://openalex.org/I32820368"]},{"raw_affiliation_string":"Institute for Brain and Intelligence, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I76569877"]}]},{"author_position":"last","author":{"id":null,"display_name":"Hanchuan Peng","orcid":null},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hanchuan Peng","raw_affiliation_strings":["Institute for Brain and Intelligence, Southeast University, Nanjing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Brain and Intelligence, Southeast University, Nanjing, China","institution_ids":["https://openalex.org/I76569877"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027506122"],"corresponding_institution_ids":["https://openalex.org/I76569877"],"apc_list":{"value":2950,"currency":"USD","value_usd":3295},"apc_paid":{"value":2950,"currency":"USD","value_usd":3295},"fwci":1.2393,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.82502337,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"17","issue":null,"first_page":"1174049","last_page":"1174049"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9944999814033508,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.0012000000569969416,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.8286826610565186},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.7301243543624878},{"id":"https://openalex.org/keywords/morphology","display_name":"Morphology (biology)","score":0.6889728307723999},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6113799214363098},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4672626852989197},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1496981978416443},{"id":"https://openalex.org/keywords/paleontology","display_name":"Paleontology","score":0.07986477017402649},{"id":"https://openalex.org/keywords/botany","display_name":"Botany","score":0.06358596682548523}],"concepts":[{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.8286826610565186},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7301243543624878},{"id":"https://openalex.org/C499950583","wikidata":"https://www.wikidata.org/wiki/Q183252","display_name":"Morphology (biology)","level":2,"score":0.6889728307723999},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6113799214363098},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4672626852989197},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1496981978416443},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.07986477017402649},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.06358596682548523},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fninf.2023.1174049","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3389/fninf.2023.1174049","pdf_url":"https://www.frontiersin.org/articles/10.3389/fninf.2023.1174049/pdf","source":{"id":"https://openalex.org/S179816892","display_name":"Frontiers in Neuroinformatics","issn_l":"1662-5196","issn":["1662-5196"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Neuroinformatics","raw_type":"journal-article"},{"id":"pmid:37388757","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37388757","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in neuroinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10303825","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10303825","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10303825/pdf/fninf-17-1174049.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Neuroinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:f889d7bd2f18477ca984fda582b355dc","is_oa":true,"landing_page_url":"https://doaj.org/article/f889d7bd2f18477ca984fda582b355dc","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Neuroinformatics, Vol 17 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fninf.2023.1174049","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3389/fninf.2023.1174049","pdf_url":"https://www.frontiersin.org/articles/10.3389/fninf.2023.1174049/pdf","source":{"id":"https://openalex.org/S179816892","display_name":"Frontiers in Neuroinformatics","issn_l":"1662-5196","issn":["1662-5196"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Neuroinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2623765598","display_name":null,"funder_award_id":"2242022R10089","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3124497070","display_name":null,"funder_award_id":"U20A6005","funder_id":"https://openalex.org/F4320336213","funder_display_name":"National Natural Science Foundation of China-Guangdong Joint Fund"},{"id":"https://openalex.org/G569996611","display_name":null,"funder_award_id":"32071367","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6328221217","display_name":null,"funder_award_id":"2018B030331001","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G6848379360","display_name":null,"funder_award_id":"U20A6005","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8527072582","display_name":null,"funder_award_id":"2018B030331001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321883","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null},{"id":"https://openalex.org/F4320336213","display_name":"National Natural Science Foundation of China-Guangdong Joint Fund","ror":null},{"id":"https://openalex.org/F4320336405","display_name":"Special Project for Research and Development in Key areas of Guangdong Province","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4380685989.pdf","grobid_xml":"https://content.openalex.org/works/W4380685989.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1508135620","https://openalex.org/W1885626623","https://openalex.org/W1965210407","https://openalex.org/W1989396876","https://openalex.org/W1992621211","https://openalex.org/W1998874218","https://openalex.org/W2011650974","https://openalex.org/W2014281241","https://openalex.org/W2047951563","https://openalex.org/W2062450961","https://openalex.org/W2124257654","https://openalex.org/W2138342944","https://openalex.org/W2156012604","https://openalex.org/W2156114286","https://openalex.org/W2157408013","https://openalex.org/W2256981962","https://openalex.org/W2467946152","https://openalex.org/W2587001086","https://openalex.org/W2600862990","https://openalex.org/W2744478946","https://openalex.org/W2789904724","https://openalex.org/W2925806435","https://openalex.org/W2966593583","https://openalex.org/W3001577996","https://openalex.org/W3035714866","https://openalex.org/W3080232649","https://openalex.org/W3083082167","https://openalex.org/W3094232608","https://openalex.org/W3156926590","https://openalex.org/W3199684914","https://openalex.org/W3202358235","https://openalex.org/W4210353766","https://openalex.org/W4210696549","https://openalex.org/W4221083769","https://openalex.org/W4226409723","https://openalex.org/W4312195824","https://openalex.org/W4366162939","https://openalex.org/W6851972685"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Background:":[0],"Neuron":[1],"morphology":[2,19,48,155],"analysis":[3,20],"is":[4],"an":[5,145],"essential":[6],"component":[7],"of":[8,38,56,73,88,94],"neuron":[9,33,47,154],"cell-type":[10],"definition.":[11],"Morphology":[12],"reconstruction":[13,25,40,49,62,78],"represents":[14],"a":[15,45],"bottleneck":[16],"in":[17,31,77,82],"high-throughput":[18],"workflow,":[21],"and":[22,29,63,97,116,119,135],"erroneous":[23,60,74,112],"extra":[24,61,75,113],"owing":[26],"to":[27,52],"noise":[28,81],"entanglements":[30],"dense":[32],"regions":[34],"restricts":[35],"the":[36,54,69,83,100],"usability":[37,55],"automated":[39],"results.":[41],"We":[42],"propose":[43],"SNAP,":[44],"structure-based":[46],"pruning":[50,118,131],"pipeline,":[51],"improve":[53],"results":[57,125],"by":[58,80],"reducing":[59],"splitting":[64],"entangled":[65],"neurons.":[66],"Methods:":[67],"For":[68],"four":[70],"different":[71],"types":[72],"segments":[76],"(caused":[79],"background,":[84],"entanglement":[85,91,98],"with":[86,92,132],"dendrites":[87],"close-by":[89],"neurons,":[90,96],"axons":[93],"other":[95],"within":[99],"same":[101],"neuron),":[102],"SNAP":[103,151],"incorporates":[104],"specific":[105],"statistical":[106],"structure":[107],"information":[108],"into":[109],"rules":[110],"for":[111,148],"segment":[114],"detection":[115],"achieves":[117],"multiple":[120,141],"dendrite":[121],"splitting.":[122],"Results:":[123],"Experimental":[124],"show":[126],"that":[127],"this":[128],"pipeline":[129],"accomplishes":[130],"satisfactory":[133],"precision":[134],"recall.":[136],"It":[137],"also":[138],"demonstrates":[139],"good":[140],"neuron-splitting":[142],"performance.":[143],"As":[144],"effective":[146],"tool":[147],"post-processing":[149],"reconstruction,":[150],"can":[152],"facilitate":[153],"analysis.":[156]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
